Applications and software components generally include a collection of executable files that perform their own functions. For example, an application generated in MATLAB®, from The MathWorks, Inc. of Natick, Mass., which provides a technical computing environment, may contain executable files, such as M-files, MEX-files, Dynamically Linked Libraries (DLLs), Java files, etc. If the application consists of a large number (e.g., hundreds or more) of executable files, deploying and distributing all of the files individually to an application user may create problems in the version control and file management of the application. In particular, the provider of the MATLAB®—based application may not modify some of the executable files in the application, such as DLLs and Java files, and add version information to the executable files. Thus, versioning each of the executable files individually is impractical. Also, storing each of the executable files individually in an application user's file system forces the application user to manage the files individually rather than being able to treat the collection of executable files as a single unit. In addition, the provider may wish to hide or conceal the contents of human readable executable files (M-files, in particular) and most conventional deployment technologies do not employ strong encryption.